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2016-10-05	Jim Procter	JAL-2252 workaround for link checker not recognising...	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 updated third party licenses	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 release notes	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2036 rebuild menus for each panel before adding...	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 release notes	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 tidy up release notes	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 tweak ensembl release notes	commit \| commitdiff \| tree
2016-10-05	Jim Procter	Merge branch 'releases/Release_2_10_Branch' into develop	commit \| commitdiff \| tree
2016-10-05	Jim Procter	Merge branch 'develop' into releases/Release_2_10_Branch	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 formatting and release notes	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 license header	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 apply license	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 format help	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 format tests	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 formatting and GPL	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 source formatting	commit \| commitdiff \| tree
2016-10-05	Jim Procter	Revert "JAL-2245 Castor mapping and code changes for...	commit \| commitdiff \| tree
2016-10-05	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 release notes/whats new	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 JAL-2152 Chimera 1.11.1 minimum version requirement	commit \| commitdiff \| tree
2016-10-04	Jim Procter	Merge branch 'releases/Release_2_10_Branch' into develop	commit \| commitdiff \| tree
2016-10-04	Jim Procter	JAL-2189 release notes	commit \| commitdiff \| tree
2016-10-04	Jim Procter	JAL-2189 link to feature sorting documentation	commit \| commitdiff \| tree
2016-10-04	Jim Procter	JAL-2189 JAL-2005 mention alignment order preservation...	commit \| commitdiff \| tree
2016-10-04	Jim Procter	JAL-2189 release notes	commit \| commitdiff \| tree
2016-10-04	Jim Procter	JAL-2005 JAL-599 test alignment and features for checking...	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2189 update RELEASE file	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2189 more release notes	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2189 ensembl sequence fetching, locus view and...	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2189 release notes	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2210 use addDBRef to ensure normalisation (just...	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2210 need to add both transcript and product, and...	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2210 JAL-2232 remove version number from ENACDS...	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2210 hack to remove EMBL from Protein crossrefs...	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2210 explicit ‘doNotAdd’ list to prevent sequences...	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2210 first pass at attempting to fix CrossRef tests...	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2210 remove ENSEMBL from protein DB list:	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2210 two pass attempt to import retrieved sequences...	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2210 try to merge all sequences referenced by a...	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2210 comments	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2210 discover candidate dataset sequences for an...	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2079 pass server name when reporting FTS ‘warning...	commit \| commitdiff \| tree
2016-10-01	Jim Procter	Merge branch 'develop' into bug/JAL-2210_ensembl_uniprot_pri...	commit \| commitdiff \| tree
2016-10-01	Jim Procter	JAL-2210 factored out code for processing cross-referenced...	commit \| commitdiff \| tree
2016-10-01	Jim Procter	JAL-2210 refactor code to remove from a list of dbrefs...	commit \| commitdiff \| tree
2016-09-30	Jim Procter	JAL-2210 some DBRef xref/ref correspondences may add...	commit \| commitdiff \| tree
2016-09-30	Jim Procter	JAL-2210 CrossRef.findInDataset should search for presence...	commit \| commitdiff \| tree
2016-09-30	Jim Procter	JAL-2210 add uniprot+mapping between ENST and ENSP...	commit \| commitdiff \| tree
2016-09-30	Jim Procter	JAL-2238 release notes	commit \| commitdiff \| tree
2016-09-30	Jim Procter	JAL-2236 release notes and additional docs	commit \| commitdiff \| tree
2016-09-30	Jim Procter	Merge branch 'develop' into releases/Release_2_10_Branch	commit \| commitdiff \| tree
2016-09-29	Jim Procter	JAL-2089 fix broken help link	commit \| commitdiff \| tree
2016-09-29	Jim Procter	Merge branch 'patch/JAL-2236_filtercolumns_seqassoc...	commit \| commitdiff \| tree
2016-09-29	Jim Procter	JAL-2236 include associated sequence id for annotation...	commit \| commitdiff \| tree
2016-09-29	Jim Procter	Merge branch 'patch/JAL-2238_tcoffee_subgroups' into...	commit \| commitdiff \| tree
2016-09-29	Jim Procter	JAL-2236 fix: bail if no context available for subgroup	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2210 patch network test for additional refs	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2210 JAL-2235 fix deriveSequence test for tightened...	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-1270 read test props before manipulating config...	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2235 patch tests where self-reference was used...	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2235 implicit test to check that exception is raised...	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2235 raise exceptions if self reference or reference...	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2210 patch for when no DBRefs on sequence	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2210 instrument setDBRefs to call ensurePrimaries	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2210 JAL-2232 check response code before attempting...	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2232 extract EMBLCDS refs from EMBL refs on Uniprot...	commit \| commitdiff \| tree
2016-09-27	Jim Procter	Merge branch 'develop' into bug/JAL-2210_ensembl_uniprot_pri...	commit \| commitdiff \| tree
2016-09-27	Jim Procter	JAL-2210 formatting	commit \| commitdiff \| tree
2016-09-27	Jim Procter	JAL-2210 report stack trace for unexpected exceptions	commit \| commitdiff \| tree
2016-09-27	Jim Procter	JAL-2210 promote direct dbrefs from verified sources...	commit \| commitdiff \| tree
2016-09-27	Jim Procter	JAL-2210 resolve todo - addDBRef adds to dataset sequence...	commit \| commitdiff \| tree
2016-09-26	Jim Procter	JAL-2148 release notes	commit \| commitdiff \| tree
2016-09-24	Jim Procter	Merge branch 'releases/Release_2_10_Branch' into develop	commit \| commitdiff \| tree
2016-09-24	Jim Procter	JAL-1919 whats new link	commit \| commitdiff \| tree
2016-09-23	Jim Procter	JAL-1957 JAL-1479 tweak SIFTS mappings documentation...	commit \| commitdiff \| tree
2016-09-23	Jim Procter	JAL-1957 JAL-1479 mention SIFTS mappings in PDB Structure...	commit \| commitdiff \| tree
2016-09-23	Jim Procter	JAL-1957 release notes	commit \| commitdiff \| tree
2016-09-23	Jim Procter	JAL-1962 release notes	commit \| commitdiff \| tree
2016-09-23	Jim Procter	JAL-2214 fix docs (consistent and correct base pair...	commit \| commitdiff \| tree
2016-09-23	Jim Procter	Merge branch 'develop' into releases/Release_2_10_Branch	commit \| commitdiff \| tree
2016-09-23	Jim Procter	JAL-2189 JAL-1479 JAL-1491 JAL-1827 release notes	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2275 release notes	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2151 release notes	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2168 -news release notes	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-1557 release notes	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2189 bumped date to 27th September \o/	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2189 JAL-1812 JAL-2068 new groovy docs (new files...	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2189 JAL-2092 popup show/hide cols with feature...	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2189 JAL-2077 note about CTRL-Click to right click...	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2189 tidy up docs	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-1812 JAL-1868 release notes	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2189 JAL-1812 JAL-2068 new groovy doc section and...	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-2189 JAL-2171 JAL-2214 JAL-1841 JAL-2215 release...	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-1841 JAL-2214 updated RNA Structure Consensus documentation	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-2214 JAL-1841 compute canonical, canonicalAndWobble...	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-1841 JAL-2215 add the ‘ignore gaps’ structure consensus...	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-2214 test for strict Watson-Crick pairing	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-2215 fix - trigger alignment update when ‘ignore...	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-2189 reworked annotation docs	commit \| commitdiff \| tree
2016-09-21	Jim Procter	Merge branch 'develop' into releases/Release_2_10_Branch	commit \| commitdiff \| tree
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